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The Complex Truth About ‘Junk DNA’

quantamagazine.org

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Re: The Complex Truth About ‘Junk DNA’

#21

Post by otherme123 »

f6v wrote: post #7
rflrob wrote: post #2

Paragraph 4: “Slowly, slowly, slowly, the terminology of ‘junk DNA’ [has] started to die,” Rest of the article: continues to use the term "Junk DNA".

Everyone doing biology professionally already knows the non-coding DNA has function. It’s only logical since we know that resource-intensive mechanisms don’t survive the evolutionary pressure if there’s no benefit for them to exist. So it’d be wasteful to replicate 98% of DNA if it’s not functional. Keep in mind it’s not only replicated, there’s error-correction as well.

If the organism is pressured, the non-coding DNA slowly fades. There are some parasitic organisms (eg Nasuia deltocephalinicola) that have highly compacted DNA: no introns, no regulatory regions, no transposable elements and even overlapping genes.

Re: The Complex Truth About ‘Junk DNA’

#22

Post by throw3849 »

jes wrote: post #16

Since I learned of this so-called Junk DNA, I assumed that one function of it might be to dilute the density of critical DNA sequences. In other words, if every base pair matters, then DNA damage from, say, ionizing radiation is more likely to be a problem than if only 1/100 base pairs matter.

Not really. Smaller DNA means smaller surface, and less total accidents.

Re: The Complex Truth About ‘Junk DNA’

#24

Post by thriftwy »

Non-coding DNA before a protein coding sequence has a very important function obvious to any programmer: It is a large section of pattern-matching "if"s.

Depending on the current state of the cell, various proteins will bind to the DNA in these places to either increase or restrict production of this specific protein. This allows multi-stage configuration of cellular protein production.

If this won't be the case, the cell will produce an equal amount of all coded proteins, which would be silly.

Source: something I learned while helping with coding for a paper in biology.

Re: The Complex Truth About ‘Junk DNA’

#25

Post by thaumasiotes »

taneq wrote: post #12
dekhn wrote: post #9

Earlier quoted context omitted.

it's wasteful to replicate non-functional DNA, yet there are organisms whose genomes are 10X-100X larger than any others (literally ten copies of a genome), and they do just fine ( https://en.wikipedia.org/wiki/Paris_japonica ). The cost of DNA replication isn't that strong a functional selection afaict.

Sounds like "non-functional DNA" might in fact have a function, hm?

Non-functional DNA is to all DNA as source code that doesn't call I/O is to all source code.

Re: The Complex Truth About ‘Junk DNA’

#26

Post by nitrogen »

throw3849 wrote: post #22
jes wrote: post #16

Since I learned of this so-called Junk DNA, I assumed that one function of it might be to dilute the density of critical DNA sequences. In other words, if every base pair matters, then DNA damage from, say, ionizing radiation is more likely to be a problem than if only 1/100 base pairs matter.

Not really. Smaller DNA means smaller surface, and less total accidents.

Hypothetically, let's suppose risk of damage correlates with cross sectional area of DNA. It's conceivable that scaling up length with less critical segments reduces risk faster than the increasing cross section increases it.

It's an interesting idea from the OP. I'm basically imagining a box full of rope and someone is poking the box with a stick. The length of rope that can fit in the box increases faster than the box's cross section.

Re: The Complex Truth About ‘Junk DNA’

#27

Post by quickthrowman »

derbOac wrote: post #19
nextos wrote: post #5

Most genetic variants associated with common diseases fall in non-coding DNA areas, previously thought to be junk DNA. Many of these non-coding areas are actually enhancer elements. These elements produce enhancer RNA, previously thought to be noise, and regulate distant genes thanks to chromosome conformation. Chromosome conformation means DNA folds in complex 3D patterns. The interplay between chromosome conformati…

I remember talking to my colleagues about 15 years ago about trying to do research on some noncoding polymorphisms and was ridiculed. The basic response was something along the lines of "those are noncoding, why would you look at those?" as if I was an idiot who didn't understand current genetics. It's been long ago enough that I don't remember all the details, but my perspective was that it was naive and arrogant to…

> Dogmatic attitudes are surprisingly prevalent in academics.

https://en.m.wikipedia.org/wiki/Planck%27s_principle

“Science progresses one funeral at a time.”

Re: The Complex Truth About ‘Junk DNA’

#28

Post by dekhn »

phkahler wrote: post #18
dekhn wrote: post #9

Earlier quoted context omitted.

it's wasteful to replicate non-functional DNA, yet there are organisms whose genomes are 10X-100X larger than any others (literally ten copies of a genome), and they do just fine ( https://en.wikipedia.org/wiki/Paris_japonica ). The cost of DNA replication isn't that strong a functional selection afaict.

And yet we probably don't know why they have so many copies. Maybe it's a crude method of regulating the ratio of activation on genes. If a few genes are either on or off, and you want to have ratios other than 1:0 1:1 or 0:1, maybe independently activating N of the M copies can achieve that. Just speculating as to how multiple copies might be useful. You can't prove that they are "extra copies" until you understand…

While I agree in principle, it does look like in most cases, these 100X large genomes are just due to random events that haven't been selected away. Often, what you see looking at evolutionary processes at a point in time, you want to find a "reason for why it's this way", when the reason is "it was random chance". Compare deinococcus radiodurans, where there's a whole mechanism for exploiting multiple copies of the genome. Plants wiht 10X genomes don't seem to exploit that, afaict.

Re: The Complex Truth About ‘Junk DNA’

#29

Post by IncRnd »

dekhn wrote: post #20
IncRnd wrote: post #14

Earlier quoted context omitted.

You're conflating the size of a genome with the amount of DNA that is non-functional.

I'm not conflating anything. Those details are scientifically conflated (IE, they are functionally related) in a very interesting way. For exmaple, new genes probably arise from gene or genome duplications.

DNA that doesn't encode proteins is not necessarily non-functional.
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